The future of AI in biologics drug discovery

By Sam DeLuca, Ph.D. With Steven Lewis, Ph.D. and Lucas Nivon, Ph.D. In our previous article in March 2023, we discussed our experience benchmarking publicly available AI protein design tools and exploring their real world strengths and weaknesses.  Here, we want to be more speculative and lay out a vision for how we think these AI methods […]

The impact of new protein AI tools on real-world biologics discovery

Protein AI tools are useful for aggressive protein design, while physics based tools continue to be required for re-design of natural proteins for most cases By Steven Lewis, Dan Farrell, Brandon Frenz, Ragul Gowthaman, Ryan Pavlovicz, David Thieker, Indigo King, Sam DeLuca, Yifan Song, and Lucas Nivon As new tools come online daily applying deep […]

Foundation Models for Proteins: Cyrus, OpenFold and the future of biologics

Recent advances in the architecture and scale of AI are leading us from the era of narrowly focused AI (e.g. text auto-complete, immune epitope prediction in a protein sequence, antibody domain detection) to broader models with applications across domains from sales and marketing to medical diagnostics. In protein biochemistry these are the “AIFold” models such […]

Homology Modeling Update

We have updated the Homology Modeling user interface, and have added the option to load multiple sequences at once. For more information on how to load a batch of sequences into HM, click here.

New Design Tool: FLEX DESIGN

Our newest CAD design tool is called Flex Design. This is similar to our current Design tool, but allows more backbone changes to occur in the area of design. This will allow more mutations to be sampled because the backbone can adjust to changes that are larger, smaller, or have a different polar nature. The […]

New Controls for Structure Viewer

The ability to select structures to view in the center window has become easier to manipulate. When you select a collection in the left window, the structures in that collection will become listed in the center window. Previously, you were only able to select structures to see in the viewer by individually clicking the eye […]

Import Collection

You can import a collection of structures from another project. First, go to the Structure Loader tab of the project where you need the collection to end up. In the center region you will see a pull down arrow so that you can select a project. Then select from the collection pull down window. Clicking […]

Sequence Logo

Sequence Logo is a tool that can be used after running CAD Design or Flex Design. The Design methods in Bench allow for sequence mutation in the search for improved stability or affinity. The Logo plot makes it simple to visualize the sequence variation at each mutatable position once the calculation is complete. Residue mutations […]

Loop rebuild

We’ve added the Loop Rebuild action to CAD. This tool is suitable for resampling the conformations of existing loops. ‘Aggressive mode’ will delete the starting loop conformation, proceeding from scratch. …more Loop Rebuild